No, it won't.
Studying the reference manual teaches you that there is a pin multiplexer which connects pins to the different h/w building blocks. Thus, when pins 9 and 10 are muxed to the UART1 (Serial2), they can not be connected to FlexTimer0 (which handles PWM for the pins 5,6,9,10,20,21,22,23) at the same time.